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Job description We are looking for an enthusiastic, highly motivated software developer with a strong background in full-stack web applications to join our team and be the lead programmer for our data analysis web platform. The platform will host applications on the cloud providing data analytics solutions for researchers and practitioners across disciplines. As a software developer, you […]

Prof. Ioannis Tsamardinos gave a Distinguished Lecture on August 19th about: “Logic-Based Causal Discovery for Heterogeneous Datasets,” as part of the Distinguish Lecture Series organized by “Center for Causal Discovery”, University of Pittsburgh, Carnegie Mellon University, Pittsburgh Supercomputing Center and Yale University.

On the 26th of August 2016 Prof. Ioannis Tsamardinos introduces the novel field of Logic-based Integrative Causal Discovery in an invited lecture at the North Carolina State University, host Prof. Yannis Viniotis Link to the talk: video

Our post doc, Sofia Triantafillou, gave a tutorial on integrative, logic-based causal discovery in the prestigious conference “Uncertainty in Artificial Intelligence” (UAI 2016, July 25-29, NY). Take a look at the slides here (link), or wait until the video is available on UAI’ s webpage: http://www.auai.org/uai2016/tutorials.php

Giorgos Athineou, MSc student at the Computer Science Department, UOC and member of MXM group presented the paper “SCENERY: a Web-Based Application for Network Reconstruction and Visualization of Cytometry Data.” on the 10th International Conference on Practical Applications of Computational Biology & Bioinformatics that took place in Seville Spain 1-3 of June 2016.

The ETIO algorithm is a innovative causal analysis method that allows identifying causal relationships by integrating several datasets obtained under different experimental conditions. The algorithm will be presented in the prestigious ACM SIGKDD Conference on Knowledge Discovering and Data Mining (KDD 2016, 13 – 17 August). KDD is an international event that brings together the top-players in […]

Robin Mjelle, Ph.D. and researcher at the Norwegian University of Science and Technology, was awarded a first-time foundation grant of $300,000 for his innovative work in the identification of biomarkers for the early detection of lung cancer. The grant was assigned by the Bonnie J. Addario Lung Cancer Foundation (ALCF) and the International Association for the Study of Lung Cancer (IASLC). These […]

Prof. Ioannis Tsamardinos and Dr. Vincenzo Lagani will give an invited talk on “Signature discovery in multi–omics datasets, novel tools” at the 1st International NTNU Symposium on Current and Future Clinical Biomarkers of Cancer, to be held in Trondheim, Norway, June 16th – 17th. Check the symposium website for more information

Prof. Tsamardinos will present the field of logic-based integrative causal discovery during two different talks to be held in Paris, France, in the upcoming week. The talks will illustrate the characteristics of a new, logic-based approach to causal discovery, that has been partly pioneered by our group. This approach is more robust to statistical errors, makes more […]

ELIXIR is an inter-governmental organisation which builds on existing data resources and services within Europe. Its main objective is orchestrating the collection, quality control and archiving of large amounts of biological data produced by life science experiments. Prof. Tsamardinos will give an invited talk at the forthcoming meeting “In silico infrastructures for Life Science’s Big Data – and the […]

title: “Causal structure learning under unfaithfulness.” abstract:” Inferring from experimental data the causal relations among variables is a scientific important but challenging task. One of the approaches relies on the probabilistic independencies between variables. Algorithms have been designed that allow the construction of the causal model of the system. Although powerful, one of the fundamental […]

Between January 19 – 22, 2016, Yannis Pantazis attended as an invited speaker the “Uncertainty Quantification for Multiscale Stochastic Systems and Applications” workshop held at IPAM, UCLA. The title of the talk was “Sensitivity analysis, uncertainty quantification and inference in stochastic dynamics“.

The 13th Hellenic Congress of Clinical Chemistry is held in Heraklion Crete, October 29-31, 2015. MXM participates with an invited lecture by Professor Tsamardinos: “Bionformatics advances for automating predictive biomarker and biosignatures from data”. Program of the congress: program.pdf .

The EU funded STATegra project has come to its end, after three years of intense research and development of novel statistical methods for the integration of heterogeneous omics data. Information regarding the objectives of the project, the activities carried in these three years and the scientific and commercial outcomes are available on the project website: […]

The STATegra Summer School in Omics and Data Integration has been held in Benicassim, Spain, from the 7th to the 11th of September 2015, providing training to more than 30 among experimentalists and bioinformaticians in the analysis of multi-omics experiments. Further information on the summer school website: http://stategrasummerschool.com/

The second edition of the “Statistical Methods for Omics Data Integration and Analysis” conference has been held in Valencia, September 14-16, 2015. MXM has participated with a talk regarding application of data-integration methods for the analysis of public microarray data in Leukemia patients. The program of the conference and further information on SMODIA2015 website: http://smodia2015.cipf.es/

From July 1st to July 3rd, Yannis Pantazis attended the workshop “Mathematical Trends in Reaction Network Theory” at Copenhagen, Denmark. He presented a poster entitled “Pathwise Information-theoretic Metrics for Parametric Sensitivity Analysis” where the relative entropy rate and the associated path Fisher information matrix were demonstrated as a means of assessing the parameters’ sensitivities.

Our work has been awarded with the Boeringer Ingelheim Cancer Research Award (Best Abstract / Poster of the Year) 2014 from the Norwegian Lung Cancer Group. This is joint work with our NTNU collaborators involving the analysis of case-control molecular profiles of lung cancer from the HUNT biobank. For more information see http://www.nlcg.no/node/122. The poster […]

As of 1-1-2015 the Bioinformatics Laboratory of the Institute of Computer Science at the Foundation for Research and Technology, Hellas has been merged with the Computational Medicine Laboratory to yield the Computational BioMedicine Laboratory (http://www.ics.forth.gr/cbml ) . The new laboratory’s Head is Dr. Kostas Marias. As the Head of the former Bioinformatics Laboratory, I (Prof. […]

On behalf of the STATegra consortium our group participated in the organization of a workshop titled “Statistical Methods for Omics Data Integration and Analysis, SMODIA”. The workshop took place in November 10-12, 2014 in Heraklion, Crete, Greece. It was organized as part of the dissemination efforts of the STATegra FP7 EU project, titled “User-driven Development […]

Pr. Ioannis Tsamardinos is invited to give a talk at MPI for Intelligent Systems in Tuebingen. Title: Advances in Integrative Causal Analysis Abstract: We’ll present the concept and approach of Integrative Causal Analysis(INCA), where causal models and relations are induced from multiple,heterogeneous datasets. The datasets maybe heterogeneous in terms of the variable sets they measure […]

Dr. Andreas Damianou presents his work on Tuesday, June 10th , 10:00am, Seminar Room 211, STEP-C, Institute of Computer Science, Foundation for Research and Technology Hellas (FORTH). Abstract: The high dimensional and complex nature of real world data makes them difficult to visualise, understand, predict and, in general, work with. Similarly, consolidating multiple distinct but […]

On behalf of the STATegra consortium our group is participating in the organization of a workshop titled “Statistical Methods for Omics Data Integration and Analysis”. The workshop will take place in November 10-12, 2014 in Heraklion, Crete, Greece. It is organized as part of the dissemination efforts of the STATegra FP7 EU project, titled “User-driven Development […]

Professor Ioannis Tsamardinos is one of the organizers of the Paramet Summer School- Computational Sciences in Drug Discovery. The workshop will take place in Heraklion, Crete, Greece, in The Foundation for Research and Technology (FORTH), from June 30 to July 4, 2014. Professor Ioannis Tsamardinos will give a lecture on Wednesday, July 2, titled “Identification […]

Associate Professor Ioannis Tsamardinos, received an ERC Consolidator Grant through the program “IDEAS” by the European Research Council (European Research Council ERC) for his research proposal titled: “Next Generation Causal Analysis: Inspired by the Induction of Biological Pathways from Cytometry Data”. The funding of the proposal will provide an opportunity to our group to develop […]

The research grant “EPILOGEAS”, titled “Causal-Based Variable Selection for Omics Data”, which was submitted in the Operational Programme “Education and Lifelong Learning 2007-2013” – Action “Excellence II”, has been approved for funding. The project is funded by the European Social Fund (ESF) and National Resources. Beneficiary of the project is the Foundation for Research and […]

Members of the IMBB institute and of the BIL lab are currently providing an introductory course to R open to FORTH researchers/post-doc/students/staff that rare interested in approaching the R software and language for the first time. The lessons will take place in the Γ100 room at 9:15 am every Wednesday.

Our group is presenting our latest discoveries and newly developed Causal Discovery algorithms in the workshop “Case Studies of Causal Discovery with Model Search”. The presentation will be recorded and be made publicly available. Some of this work stems from a close collaboration with our Karolinska Institutet STATegra partners in the Computational Medicine Unit. The […]

Our group participated in the first year’s STATegra project meeting, held in the Imperial College London. The meeting was a great success. Novel data will be available soon, while new methods and tools are continuously being developed by the consortium. New upcoming events will be held this March. STATegra has a new, updated web-site containing […]

This year, our group’s research has transcended the computer science and bioinformatics publishing forums and, through collaborations with prestigious biological groups, has participated in publications in high-impact journals of the biology community. The Garini’s lab research has shown that that DNA damage triggers a chronic auto-inflammatory response leading to fat depletion published in Cell Metabolism. […]

BIL has recently secured funding in competitive and exciting EU and Greek National research grants (BIOSYS by GSRT, eModia by GSRT, STATegra EU FP7, as well as participation in other grants). BIL is looking to expand by hiring ambitious, energetic, intelligent, and hard-working individuals to lead the development of novel machine learning methods, particularly for […]

Our group is participating in the new institutional grant on Systems Biology, named BIOSYS, coordinated by the Institute of Molecular Biology and Biotechnology of FORTH. The grant will provide more funding for developing causal discovery algorithms, as well as model selection algorithms for machine learning models. The algorithms will be packaged in tools for non-experts […]

Members of our group gave a tutorial on Causal Discovery, titled “An Introduction to Causal Discovery, a Bayesian Network Approach” in the recent the High-Throughput Omics and Data Integration Workshop organized by the STATegra projects and the COST Action SeqAHead. Apart from the introduction to the theory and algorithms of Causal Discovery, the tutorial covered […]

Sofia Triantafillou received one of the three Best Poster Awards in the recent 7th Conference of the Hellenic Society for Computational Biology and Bioinformatics (HSCBB12) for her poster titled “Predicting associations from multiple “omics” data sets”. The judging committee of the conference consisted of all the invited speakers of the conference.

New positions are available at FORTH within our group. We have secured funding in competitive and exciting EU research grants and are looking to expand by hiring ambitious, energetic, intelligent, and hard-working individuals to lead the development of novel causal discovery and machine learning methods, particularly for bioinformatics and computational biology problems, as well as […]

Mens X Machina Probabilistic Graphical Model Toolbox 0.9.3 and Mens X Machina Common Toolbox (previously named Commons Toolbox) 0.9.3 are available for download. The toolboxes were completely rewritten and are mostly object-oriented now. Support for the MMHC algorithm and the junction-tree algorithm for structure learning and inference, respectively, was added. The toolboxes are not compatible […]

Knowledge in the form “A causes B” and “A does not cause B” is often available. For example, in an experiment where temperature (A) is controlled, then for any quantity B that changes we can infer A causes B. Our new publication in ICML shows how to incorporate such knowledge when inducing a causal models […]

Is it possible to predict a disease is correlated with an exposure factor without ever performing a study to measure them? The answer is shown to be yes, in some cases, by analyzing existing datasets that measure these two quantities, but not jointly. The idea is to induce all causal models that are simultaneously consistent […]

The STATegra collaborative FP7 proposal has been accepted for funding by the EC! Our group is a member of the STATegra consortium and will be leading the Work Package related to the development of machine learning, statistical, and data mining methods to integratively analyze heterogeneous biological datasets. STATegra funding will allow us to grow, expand, […]

Can we learn causal relationships from observations? In this 3-hour tutorial we attempt to give the intuition behind causal discovery from observational data, discuss the main assumptions, present the theory of Bayesian networks and some basic causal discovery algorithms, demonstrate some of their most successful applications to feature selection and biomedical data, and also share […]

The management of the Institute of Computer Science, Foundation of Research and Technology, Hellas has recently (Oct. 2010) decided to found the Bioinformatics Laboratory, with the Mens X Machina group members as its founding and core members and Prof. Tsamardinos as its first Head. The decision reflects the commitment of the management to progressing and […]

New versions (0.9.2) of our MATLAB® toolboxes have been released. New features in version 0.9.2 of Mens X Machina Probabilistic Graphical Model Toolbox (MxM PGM) include: Skeleton identification error estimation/calculation utilities Templates for custom functions, handles to which can be used as values of skeleton identification function parameters. New features in version 0.9.2 of Mens […]

Projects

Current

CAUSALPATH

CAUSALPATH is an European Research Council (ERC) consolidator grant focused on (a) developing Causal Analysis methods and (b) using these methods for inducing biological pathways from cytometry data. Visit CAUSALPATH’s Page

Cancer-Biomarkers in HUNT

The Cancer-Biomarkers in HUNT is an international consortium of five universities in five countries that collaborate to improve the survival of lung cancer… Visit Cancer-Biomarkers in HUNT WebPage

Previous

STATegra

The STATegra project aims to develop new statistical methods and tools for the integrative analysis of diverse omics data for a more efficient use of the genomics technologies. Visit STATegra’s page

About Us

Mens Ex Machina, Mind from the Machine or "Ο από Μηχανής Νους" paraphrases the latin expression Deus Ex Machina, God from the Machine. The name was suggested by Lucy Sofiadou, Prof. Tsamardinos' wife.

We are a research group, founded in October 2006, led by Associate Professor Ioannis Tsamardinos, interested in Artificial Intelligence, Machine Learning, and Biomedical Informatics and affiliated with the Computer Science Department of University of Crete. The group’s aims are to progress science and disseminate knowledge via educational activities and computer tools. Our group is involved in

Research:

Theoretical, algorithmic, and applied research in all of the above areas; we are also involved in interdisciplinary collaborations with biologists, physicians and practitioners from other fields.

Education:

Educational activities, such as teaching university courses, tutorials, summers schools, as well as supervising undergraduate dissertations, masters projects, and Ph.D. theses.

Systems and Software:

Implementation of tools, systems, and code libraries to aid the dissemination of the research results.Funding is provided from through the University of Crete, often originating from European and International research grants.

Current research activities include but not limited to the following:

Causal discovery methods and the induction of causal models from observational studies. Specifically, we have recently introduced the problem of Integrative Causal Analysis (INCA).